LAMP-LD – Local Ancestry Inference in Admixed populations

Software package for local ancestry inference in admixed populations. It takes as input genotype data from admixed samples and produces a local ancestry (chromosome painting) according to the ancestry at every locus in the genome. Several versions are included in the software package:

WINPOP: window-based algorithm that use an improved modeling of the recombinations events within each window. This leads to a better accuracy for recently admixed populations where the ancestral populations are closely related (e.g., European Americans or Japanese-Chinese, etc.), in case the ancestral populations are known. WINPOP does not model haplotypes and assumes SNPs to be independent conditional on their ancestry (10.1093/bioinformatics/btp197).

LAMP-LD: window-based algorithm combined within a hierarchical Hidden Markov Model to represent haplotypes in the population. It can process 2,3 or 5 mixing populations, and its short per-sample processing time makes it suitable for analyzing large datasets of dense SNP panels (10.1093/bioinformatics/bts144).

LAMP-HAP: similar to LAMP-LD but processes haplotype data when high-quality phasing is available (e.g. in families), and utilizes trio nuclear family designs to improve estimation accuracy.